Align Lactate utilization protein B (characterized)
to candidate WP_035700907.1 BA79_RS03525 iron-sulfur cluster-binding protein
Query= SwissProt::Q81GA4 (473 letters) >NCBI__GCF_000691145.1:WP_035700907.1 Length = 474 Score = 742 bits (1915), Expect = 0.0 Identities = 357/470 (75%), Positives = 413/470 (87%), Gaps = 1/470 (0%) Query: 1 MSMKISEKKFNDRVGDGIQDSFMRGAVSSAQTRLYTNRLKAADELGNWEEWRELGEQIRQ 60 MSMKI EK F +R+G+G++D+ MRGAVSSAQ RLY R+ A++ LGNWE+WRELGE IRQ Sbjct: 1 MSMKIGEKAFKERIGEGLEDAVMRGAVSSAQERLYKRRMTASEVLGNWEKWRELGEDIRQ 60 Query: 61 HTLENLDYYLMQLSENVSKRGGHVYFAKTKEEAAKYIQDVAKKKQAKKVVKSKSMVTEEI 120 HTL +LD YL QLSE+VS+RGGHV+FAKTKEEA+ YIQDVA+KK AKK+VKSKSMVTEEI Sbjct: 61 HTLAHLDDYLYQLSESVSRRGGHVFFAKTKEEASAYIQDVAQKKAAKKIVKSKSMVTEEI 120 Query: 121 SMNHALEEIGCEVLESDLGEYILQVDN-DPPSHIIAPALHKNRTQIRDVFKEKLGYENSD 179 MN ALEEIGCEV+ESDLGEYILQVD+ +PPSHI+APALH + QIR+VF EKLGY+ S+ Sbjct: 121 EMNQALEEIGCEVVESDLGEYILQVDDHEPPSHIVAPALHMTKEQIREVFHEKLGYDMSE 180 Query: 180 DPYEMTKFVRKQLREKFMDAEIGVTGCNFAVANTGSLCLVTNEGNADLVMSIPKTQIAVM 239 P EMTKFVR LREKF++A+IGVTGCNFAVA+TGS+CLVTNEGNADLV SIPKT IAVM Sbjct: 181 TPEEMTKFVRALLREKFLEADIGVTGCNFAVADTGSICLVTNEGNADLVTSIPKTHIAVM 240 Query: 240 GMERMVPTMEELDVLVGLLCRSAVGQKLTSYVTVAGPIQEEEVDGPEEFHLVVVDNGRSQ 299 GMER+VPT EELDVLVGLLCRSAVGQKLTSY++V GP E EVDGPEEFHLV+VDNGRS Sbjct: 241 GMERLVPTTEELDVLVGLLCRSAVGQKLTSYISVVGPKGEGEVDGPEEFHLVIVDNGRST 300 Query: 300 ILGSEFRSVLQCIRCAACVNVCPVYRHVGGHSYGSIYSGPIGAVLTPLLGGYDDYKELPY 359 ILG+EF+ VLQCIRCAAC+NVCPVYRHVGGHSYGSIY GPIGAVL+PLLGGYDDY+ELP+ Sbjct: 301 ILGTEFQPVLQCIRCAACINVCPVYRHVGGHSYGSIYPGPIGAVLSPLLGGYDDYQELPF 360 Query: 360 ASSLCGACTEACPVKIPLHDLLLKHRQVIVEQEGRAPLAEKLAMKMFSMGASSAALYKMG 419 ASSLC ACT+ACPVKIPLH+LL+KHRQVIVE+EGRAP AE +AMKMF MGAS+ +Y+ G Sbjct: 361 ASSLCAACTDACPVKIPLHELLIKHRQVIVEKEGRAPKAEMMAMKMFGMGASTPRMYRFG 420 Query: 420 SKMAPAAMSPFTSGNRVSKGVGPLKNWTDIREFPAPSKERFRDWYKDHKK 469 +K AP + S ++SKG GPLKNWT+IR+ PAPSKERFRDW+K +K Sbjct: 421 TKAAPVLLKRMASNGQISKGAGPLKNWTEIRDLPAPSKERFRDWFKKKQK 470 Lambda K H 0.317 0.133 0.391 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 757 Number of extensions: 29 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 473 Length of database: 474 Length adjustment: 33 Effective length of query: 440 Effective length of database: 441 Effective search space: 194040 Effective search space used: 194040 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory